By Zachary Cohen, CNN

(CNN) -- Defense Secretary James Mattis is doing his best to downplay notions that he is concerned about working with President Donald Trump's hawkish new national security adviser John Bolton despite signs of a shifting power dynamic at the highest levels of the administration and strong indications that the two men could clash over key issues like North Korea and Iran.

One of Trump's most trusted advisers, Mattis has clearly wielded significant influence since joining the administration and has demonstrated that recent staffing shakeups have done little to hurt his standing with the President.

The weight of his opinion was again on display last week when Trump begrudgingly signed a $1.3 trillion spending bill after Mattis stressed it was a national security imperative.

But the addition of Bolton, coupled with Trump's nomination of another hawk in CIA director Mike Pompeo to replace ousted Secretary of State Rex Tillerson, represents a dramatic overhaul atop the administration's national security team that many argue leaves Mattis more isolated than ever.

Mattis isolated?

Mattis lost a particularly consistent ally when Trump unceremoniously fired Tillerson earlier this month, several sources have told CNN. The two secretaries had a close relationship talking regularly and meeting for breakfast or lunch every week. They often would work out issues together and present a united position to the President.

Like Mattis, Tillerson argued against leaving the Iran nuclear deal and consistently stressed the importance of prioritizing a diplomatic resolution to tensions with North Korea, a source close to the White House told CNN.

But while Mattis has been able to navigate a complex political minefield in a way that avoids drawing the President's ire, sources close to the President told CNN that the same could not be said for Tillerson, whose firing was due in part to the fact it had become clear he was not on the same page as Trump and wanted to handle foreign policy his own way.

Additionally, Trump himself indicated that he was looking for a secretary of state who aligned with his own way of thinking -- noting that he and Pompeo are "on the same wavelength" and "the relationship has always been very good and that is what I need."

Initially there was also a concern that Bolton had not made it clear enough that, if tapped as national security adviser, he would "absolutely go along with Trump," a source close to Bolton told CNN.

Ultimately, Bolton met with Trump at the White House and left with the job after he went over and above to make clear he will do exactly what Trump wants, the source said.

Sources previously told CNN that Pentagon assisted the White House in an effort to transition McMaster out of his role of national security adviser by prospecting potential four-star military jobs he might be suited for.

Several sources have also said that Mattis was privately opposed to the idea of picking Bolton as his replacement and tried to block him from getting the job -- though ultimately, Trump opted to go with Bolton anyway.

Throughout his career, Mattis has demonstrated that he is by no means a dove when it comes to situations that call for the use of military force but the move to bring Bolton and Pompeo into the fold has sparked concerns that he may find himself at odds with two influential advisers who have previously supported more aggressive policy stances.

And while Mattis has, to date, avoided publicly disagreeing with Trump, "he may soon have no choice but to start being more pointed in conveying his views where matters of war and peace are concerned, both behind the scenes and in public," according to Kingston Reif, the director for Disarmament and Threat Reduction Policy at the Arms Control Association.

"The departures of McMaster and Tillerson and the arrival of Bolton and (pending Senate confirmation) Pompeo, leave Mattis more isolated in the administration and will reveal just how strong his influence on the President really is," Reif said.

"At the same time these personnel changes make Mattis' voice of soberness and pragmatism all the more important, particularly on Iran and North Korea," Reif added.

Potential for conflict

Specifically, it is Bolton's hard-edged, hawkish views on issues like North Korea, Iraq, Iran and Syria that made him a controversial pick and could put him at odds with Mattis in the future -- especially with potential talks with North Korea looming.

On North Korea, Reif notes that Mattis favors a diplomatic resolution and has warned about the potentially catastrophic consequences of military action. By contrast both Bolton and Pompeo have argued that using force to prevent North Korea from acquiring the capability to strike the US homeland with nuclear weapons is preferable to deterring/containing that threat, he said.

There are similar disagreements over the Iran deal as "Mattis believes the United States should continue adhering to the agreement, while Pompeo and Bolton have advocated abrogating it," he said.

But while it's possible that Mattis may disagree with Bolton or Pompeo at times, Behnam Ben Taleblu of the Foundation for Defense of Democracies argues that it is not a forgone conclusion that different personalities are going to clash over policy.

"Ultimately the buck stops at the President," Taleblu said, adding that as long as all three are working toward implementing Trump's policy objectives there should be little reason for conflict.

For now, both Mattis and Bolton have said they are optimistic about the road ahead despite their philosophical differences on many of the most urgent foreign policy challenges currently facing the Trump administration.

Speaking publicly for the first time about the move to name Bolton as the replacement for outgoing national security adviser H.R. McMaster, Mattis said Tuesday that he looked forward to working with the former UN ambassador and that he hoped the two men held "different world views" to avoid "group think."

"I'll tell you right up front, it's going to be a partnership, we are going to go forward," Mattis told reporters at the Pentagon.

A senior defense official told CNN on Tuesday that the Pentagon does not expect conflict at this point between Mattis and Bolton because the role of national security adviser is more of an "aggregator" than a "policy adviser."

"We don't see actual changes in policy" coming down the road just because Bolton is on the job, the official said, adding that while the President can always change his mind and look for a new policy, it won't be Bolton dictating that change.

But according to Reif, the elevation of Pompeo and addition of Bolton "could not have come at a worse time given the critical and hugely consequential near-term decisions facing the President on Iran and North Korea."

According to Taleblu, Syria is one issue involving Mattis that Pompeo and Bolton may look to encourage a strategic shift on.

"So far the war in Syria has been defined by the campaign against ISIS. Pompeo and Bolton may want to signal resolve against Iran by targeting Shia militias," he said.

Nuclear diplomacy is another issue to watch -- especially given the looming May 12 Iran deal deadline -- the next date by which Trump has to waive sanctions against Iran or leave the accord, according to Taleblu.

If Trump opts to remain in the deal and signals a desire to broaden the scope of the talks to include other nations, Pompeo and Bolton would be the ones to give him the strong political cover he would be looking for, he said.